7WUR

CryoEM structure of sNS1 complexed with Fab5E3


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


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Literature

CryoEM structures of the multimeric secreted NS1, a major factor for dengue hemorrhagic fever.

Shu, B.Ooi, J.S.G.Tan, A.W.K.Ng, T.S.Dejnirattisai, W.Mongkolsapaya, J.Fibriansah, G.Shi, J.Kostyuchenko, V.A.Screaton, G.R.Lok, S.M.

(2022) Nat Commun 13: 6756-6756

  • DOI: https://doi.org/10.1038/s41467-022-34415-1
  • Primary Citation of Related Structures:  
    7WUR, 7WUS, 7WUT, 7WUU, 7WUV

  • PubMed Abstract: 

    Dengue virus infection can cause dengue hemorrhagic fever (DHF). Dengue NS1 is multifunctional. The intracellular dimeric NS1 (iNS1) forms part of the viral replication complex. Previous studies suggest the extracellular secreted NS1 (sNS1), which is a major factor contributing to DHF, exists as hexamers. The structure of the iNS1 is well-characterised but not that of sNS1. Here we show by cryoEM that the recombinant sNS1 exists in multiple oligomeric states: the tetrameric (stable and loose conformation) and hexameric structures. Stability of the stable and loose tetramers is determined by the conformation of their N-terminal domain - elongated β-sheet or β-roll. Binding of an anti-NS1 Fab breaks the loose tetrameric and hexameric sNS1 into dimers, whereas the stable tetramer remains largely unbound. Our results show detailed quaternary organization of different oligomeric states of sNS1 and will contribute towards the design of dengue therapeutics.


  • Organizational Affiliation

    Programme in Emerging Infectious Diseases, Duke-National University of Singapore Medical School, Singapore, 169857, Singapore.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Core protein
A, B
341dengue virus type 2Mutation(s): 0 
UniProt
Find proteins for D3XNS4 (dengue virus type 2)
Explore D3XNS4 
Go to UniProtKB:  D3XNS4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD3XNS4
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Fab 5E3 Heavy ChainC [auth E],
E [auth G]
118Homo sapiensMutation(s): 0 
Entity Groups  
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Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Fab 5E3 Light ChainD [auth F],
F [auth H]
108Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Research Foundation (NRF, Singapore)SingaporeNRF-NRFI2016-01

Revision History  (Full details and data files)

  • Version 1.0: 2022-12-21
    Type: Initial release